{"schema_version":1,"research_id":"eoa_inverse_innovation_exp06_external_evaluation_20260803","source_assessment_id":"representation_independent_interface_contract__nanotechnology:P2:v0","cell_id":"representation_independent_interface_contract__nanotechnology","search_queries":["scanning probe microscope control software hardware independent modular automation controller API state fault completion","atomic force microscope open source control software hardware independent controller automation","Nanonis programming interface TCP protocol Z controller official","ISO scanning probe microscopy automation control interface standard","site:beilstein-journals.org \"afspm\" manufacturer-agnostic automation scanning probe microscopy","site:specs.zhinst.com SPM controller API approach retract status fault AFM official","site:nanonis.com programming interface TCP commands ZCtrl Withdraw Home official PDF","scanning probe microscope autonomous control safety collision tip sample automation faults paper","Nanonis TCP protocol PDF ZCtrl Withdraw command official SPECS","site:support.specs-group.com nanonis programming interface TCP protocol command reference","site:github.com/afspm afspm translator test suite generic microscope commands","atomic force microscopy automation tip sample damage safety autonomous operation paper","SiLA 2 command execution lifecycle state cancellation official standard lab automation","site:sila-standard.com specification command execution status cancel error SiLA 2","OPC UA laboratory device command state machine standard motion safety","ROS 2 lifecycle node action goal states cancel result official design","site:specs-group.com/nanonis/downloads TCP Programming Interface PDF Nanonis","site:specs-group.com nanonis TCP protocol ZCtrl.Withdraw","Nanonis programming interface official TCP protocol","Grutter Group afspm GitHub","github afspm manufacturer agnostic scanning probe microscopy translator test suite","\"Automation of an atomic force microscope via Arduino\" DOI","site:sciencedirect.com \"Automation of an atomic force microscope via Arduino\"","ISO 28600:2011 official scanning probe microscopy data transfer format","OPC UA LADS v1.0 publication date 30500-1","SiLA 2 Part B Mapping Specification v1.1 publication date"],"sources":[{"source_id":"S1","title":"afspm: A framework for manufacturer-agnostic automation in scanning probe microscopy","publisher":"Beilstein-Institut, Beilstein Journal of Nanotechnology","url":"https://www.beilstein-journals.org/bjnano/articles/17/45","source_class":"PRIMARY_RESEARCH","publication_date":"2026-05-18","accessed_at":"2026-08-03","claims_supported":["SPM automation is time-consuming, expertise-intensive, and difficult to reuse across manufacturers.","afspm already supplies generic commands and data structures, manufacturer-specific translators, process mediation, configuration-driven automation, and an automated translator test suite.","The framework was integrated with Nanonis, Scienta Omicron, GXSM, and Asylum Research controllers and tested using a Nanonis simulator and physical experiments.","A controller version lacking scan-stop capability failed two translator tests, demonstrating that superficially similar interfaces can have consequential semantic and version differences.","The Grutter Group and National Research Council Canada are identifiable developers and funders expressing a need for reusable manufacturer-agnostic SPM automation."]},{"source_id":"S2","title":"Automation of an atomic force microscope via Arduino","publisher":"Elsevier, HardwareX","url":"https://www.sciencedirect.com/science/article/pii/S2468067223000548","source_class":"PRIMARY_RESEARCH","publication_date":"2023-06-29","accessed_at":"2026-08-03","claims_supported":["Legacy AFM automation may depend on emulated keyboard commands and sparse controller feedback.","The reported workaround automated a Dimension 3000 AFM for under $60, while the authors described standard AFMs as approximately half-million-dollar instruments.","The implementation shows both demand for unattended AFM automation and the broad cost heterogeneity between software workarounds and instrument replacement."]},{"source_id":"S3","title":"Evaluating large language model agents for automation of atomic force microscopy","publisher":"Springer Nature, Nature Communications","url":"https://www.nature.com/articles/s41467-025-64105-7","source_class":"PRIMARY_RESEARCH","publication_date":"2025-10-14","accessed_at":"2026-08-03","claims_supported":["AFM API commands directly produce physical instrument movement, making command authorization and sequencing safety-relevant.","The study observed unauthorized or extraneous AFM actions and concluded that robust benchmarking and operational guardrails are necessary.","The authors separated general from critical AFM operations, restricted critical functions to trained experts, and noted that minor errors in calibration-related operations could seriously damage the instrument."]},{"source_id":"S4","title":"Programming interface","publisher":"SPECS Surface Nano Analysis GmbH, Nanonis","url":"https://www.specs-group.com/nanonis/products/detail/programming-interface-2/","source_class":"OFFICIAL_PRODUCT_DOCUMENTATION","publication_date":"undated","accessed_at":"2026-08-03","claims_supported":["A commercial SPM controller exposes broad LabVIEW and TCP programming interfaces across multiple languages.","The interface supports programmatic scanning, manipulation, auto-approach, tip cleaning, scanner switching, and other physically consequential functions.","SPECS explicitly supports offline routine development with a Nanonis STM simulator, supporting the feasibility of a hardware-disconnected first test."]},{"source_id":"S5","title":"ISO 28600:2011 — Surface chemical analysis — Data transfer format for scanning-probe microscopy","publisher":"International Organization for Standardization","url":"https://www.iso.org/standard/44808.html","source_class":"STANDARD","publication_date":"2011-07","accessed_at":"2026-08-03","claims_supported":["An existing SPM interoperability standard governs transfer of imaging and spectroscopy data.","Its published scope is data transfer rather than controller command lifecycle, fault recovery, physical side effects, or behavioral substitution, leaving the proposed control-contract question outside this standard's stated scope."]},{"source_id":"S6","title":"OPC UA for Laboratory & Analytical Device Standard (LADS), Part 1: Basics, v1.0.0","publisher":"OPC Foundation","url":"https://reference.opcfoundation.org/specs/OPC-30500-1/4.1.3.2","source_class":"STANDARD","publication_date":"2023-11-30","accessed_at":"2026-08-03","claims_supported":["Laboratory-device standardization already uses domain-facing device state machines that abstract internal device state.","LADS includes controller functions, device health, programs, profiles, and conformance units, making it close architectural prior art for a state-based laboratory-device contract.","LADS is generic and does not itself define the proposed SPM approach, engagement, scan, retraction, envelope, or sensor-confirmation semantics."]},{"source_id":"S7","title":"SiLA 2 Part B — Mapping Specification v1.1","publisher":"SiLA Consortium","url":"https://sila-standard.com/wp-content/uploads/2022/03/SiLA-2-Part-B-Mapping-Specification-v1.1.pdf","source_class":"STANDARD","publication_date":"2022-03","accessed_at":"2026-08-03","claims_supported":["A laboratory-automation standard already distinguishes command initiation, execution observation, and result retrieval.","SiLA observable commands expose waiting, running, finished-successfully, and finished-with-error states plus execution identifiers, progress, timing, and errors.","These generic command-lifecycle semantics overlap materially with the proposal but do not supply its SPM-specific physical-state invariants or qualification oracle."]},{"source_id":"S8","title":"ROS 2 Actions design specification","publisher":"Open Robotics / ROS 2","url":"https://design.ros2.org/articles/actions.html","source_class":"OFFICIAL_GUIDANCE","publication_date":"2020-05","accessed_at":"2026-08-03","claims_supported":["Established robotics middleware already models long-running operations with separate goal acceptance, execution feedback, result retrieval, cancellation, and terminal outcomes.","ROS 2 Actions use explicit ACCEPTED, EXECUTING, CANCELING, SUCCEEDED, ABORTED, and CANCELED states.","This provides mature adjacent implementation machinery but no SPM-specific envelope, calibration, fault-closure, retraction, or sensor-confirmed-completion contract."]}],"problem_evidence":{"support":"STRONG","rationale":"The problem is directly visible. afspm documents manufacturer-specific scripts, cross-language/controller differences, incomplete stop capability, and a need for manufacturer-agnostic automation. The Arduino study shows a legacy system controlled through keyboard emulation and sparse feedback. The Nature study demonstrates that automated AFM commands cause physical motion and that unauthorized actions create equipment-safety concerns. What remains unmeasured is the prevalence and cost of actual controller-substitution failures across laboratories.","source_ids":["S1","S2","S3","S4"]},"stakeholder_evidence":{"support":"MODERATE","rationale":"The Grutter Group/NRC team is an identifiable maintainer and funded developer that explicitly seeks reusable manufacturer-agnostic SPM automation; SPECS provides automation APIs and offline simulation; AFM researchers have called for robust safety protocols. These are credible prospective adopters, implementers, or authorizers, but no source commits any organization to adopt this particular ProbeManipulationSession contract.","source_ids":["S1","S3","S4"]},"prior_art":{"proximity":"SUBSTANTIAL_COLLISION","closest_analogues":[{"name":"afspm","similarity":"Exact-domain manufacturer-agnostic SPM commands, controller translators, mediation, automated translator tests, simulation, and multi-controller validation.","remaining_difference":"Its reported base-operation tests do not establish the proposal's full SPM physical lifecycle, envelope invariants, FAULT closure, sensor-confirmed completion rule, side-effect matrix, or mutation-tested behavioral-substitution acceptance rule.","source_ids":["S1"]},{"name":"OPC UA LADS","similarity":"Standardized laboratory-device abstraction with device and control-function state machines, health information, profiles, and conformance units.","remaining_difference":"It is a generic laboratory-device information model rather than an SPM manipulation-session behavioral profile with probe-specific physical invariants.","source_ids":["S6"]},{"name":"SiLA 2 observable commands","similarity":"Standard command identity, asynchronous execution observation, progress, success/error distinction, and separate result retrieval.","remaining_difference":"It does not define the proposed SPM-wide engagement and fault state machine, bounded-motion envelope, retraction obligation, or physical qualification boundary.","source_ids":["S7"]},{"name":"ROS 2 Actions","similarity":"Established representation-independent pattern for acceptance, execution, feedback, cancellation, abort, and terminal results.","remaining_difference":"It supplies transport-level action lifecycle semantics, not SPM-specific safety state, calibration provenance, side-effect limits, or laboratory authorization.","source_ids":["S8"]},{"name":"Nanonis programming interface and simulator","similarity":"Commercial SPM API and offline simulator spanning scans, manipulation, approach, and controller utilities.","remaining_difference":"It is a vendor-specific implementation surface rather than a cross-vendor behavioral contract or reusable conformance oracle.","source_ids":["S4"]}],"distinctive_claim_remaining":"Relative to afspm's existing generic command/translator tests and generic LADS, SiLA, or ROS lifecycles, an SPM-specific opaque contract that binds command admissibility, sensor-confirmed completion, FAULT closure, authorized envelopes, retraction outcomes, and physical side-effect limits will detect safety-relevant non-substitutability that those comparators miss without exposing vendor-specific fields. This is falsified if the candidate finds no additional defects, requires vendor fields on the public surface, rejects valid representation changes excessively, or lets a held-out lifecycle or side-effect violation pass.","confidence":"HIGH"},"implementation_evidence":{"support":"MODERATE","rationale":"The software architecture is credible: afspm already implements generic commands, four translator types, automated tests, and simulator integration; Nanonis officially supports offline simulator development; LADS, SiLA, and ROS provide reusable state/action patterns. Workflow feasibility is therefore good for a disconnected prototype. Data normalization, calibration provenance, cross-modality state completeness, cybersecurity, and physical qualification remain unresolved. Legal authority is laboratory- and institution-specific; the Nature study supports restricting critical AFM operations to trained experts but does not establish a universal approval regime.","source_ids":["S1","S3","S4","S6","S7","S8"]},"scores":{"meaningful_impact":{"score":4,"rationale":"Incorrect sequencing or unauthorized motion can damage instruments, tips, samples, or data validity, although incident prevalence and avoided losses are not quantified.","source_ids":["S1","S3"]},"stakeholder_pull":{"score":4,"rationale":"A funded team has already built manufacturer-agnostic SPM automation and invited collaboration, and a controller vendor supports APIs and simulation. Pull for this stricter semantic layer is inferred rather than committed.","source_ids":["S1","S4"]},"incremental_advantage":{"score":3,"rationale":"SPM-specific physical invariants and mutation-tested substitution could improve on existing translator sanity tests, but no comparative evidence yet shows additional defect detection or lower integration effort.","source_ids":["S1","S6","S7","S8"]},"distinctiveness_plausibility":{"score":2,"rationale":"The proposal combines well-established action/state-machine standards with afspm's already close domain implementation. The remaining SPM-specific semantic profile is plausible but narrow.","source_ids":["S1","S6","S7","S8"]},"technical_implementability":{"score":4,"rationale":"Existing generic SPM translators, test suites, simulators, IDLs, and action-state patterns make a software-only implementation technically credible.","source_ids":["S1","S4","S6","S7","S8"]},"adoption_authority_feasibility":{"score":3,"rationale":"Software stewards can run a disconnected trial, but physical use requires instrument-owner and trained-expert approval, and no prospective adopter has accepted the proposed governance role.","source_ids":["S1","S3"]},"evidence_readiness":{"score":4,"rationale":"Open afspm code, existing translator tests, official simulator support, and mature standards provide immediate comparators and test infrastructure.","source_ids":["S1","S4","S6","S7","S8"]},"safety_net_benefit":{"score":4,"rationale":"A disconnected simulator trial, explicit authority boundary, and pre-registered invariant tests provide a strong reversible first step; simulation cannot establish physical safety.","source_ids":["S1","S3","S4"]},"scalability":{"score":3,"rationale":"A shared oracle can scale across implementations, but each controller and SPM modality may require costly semantic mapping, calibration handling, and qualification.","source_ids":["S1","S4"]}},"score_confidence":"MODERATE","costs":{"first_evidence":{"band_2026_usd":"50K_TO_250K","scope":"Eight-to-twelve-week software-only contract differentiation trial: transition model, two independently implemented simulators, comparator adapters, seeded mutants, generated and held-out tests, and leakage audit.","confidence":"MODERATE","assumptions":["Approximately 12–24 person-weeks across an instrument-control engineer, independent simulator implementer, SPM domain expert, and test lead.","No hardware connection, instrument purchase, vendor certification, or regulated quality-system validation.","Resource-equivalent cost includes loaded labor, review, compute, and contingency rather than cash expenditure alone."],"source_ids":["S1","S4"]},"initial_deployment_startup":{"band_2026_usd":"250K_TO_1M","scope":"Productionize one contract version for two controller families, including hardened adapters, safety analysis, diagnostics, documentation, test fixtures, security review, and laboratory quality/safety approval preparation.","confidence":"LOW","assumptions":["Two materially different controller integrations.","Existing instruments and vendor API licenses are available.","Physical qualification and instrument downtime are excluded from this startup band."],"source_ids":["S1","S3","S4"]},"operational_launch":{"band_2026_usd":"250K_TO_1M","scope":"Authority-controlled launch at one laboratory: bench and hardware qualification, calibration and envelope validation, monitored procedure migration, operator training, rollback drills, and staged acceptance.","confidence":"LOW","assumptions":["One laboratory and a small set of procedures.","No new AFM purchase; the Arduino paper indicates that instrument replacement can otherwise approach a much larger capital scale.","Instrument owner permits controlled qualification and vendor support is available."],"source_ids":["S1","S2","S3","S4"]},"annual_recurring":{"band_2026_usd":"50K_TO_250K","scope":"Contract stewardship, regression and nightly compatibility testing, controller-version maintenance, incident review, deprecation governance, and annual safety/quality review for a small deployment.","confidence":"LOW","assumptions":["Two to four maintained controller adapters.","Part-time software steward plus SPM and safety-review effort.","Excludes major controller rewrites, new instrument purchases, and physical consumables."],"source_ids":["S1","S3","S4"]}},"verified_pipeline_gates":{"externally_supported_problem":{"status":"YES","reason":"Independent research and vendor documentation visibly establish controller heterogeneity, legacy feedback limitations, direct physical consequences of API actions, and safety concerns in automated AFM.","source_ids":["S1","S2","S3","S4"]},"externally_credible_adopter_or_authorizer":{"status":"YES","reason":"The Grutter Group/NRC afspm maintainers are identifiable, funded implementers explicitly seeking reusable cross-controller automation; SPECS is a credible implementation stakeholder. This verifies a plausible adopter class, not an adoption commitment.","source_ids":["S1","S4"]},"distinct_testable_incremental_claim":{"status":"YES","reason":"The remaining claim is explicitly comparative against afspm translator tests and generic lifecycle standards and can be tested with seeded semantic faults, held-out command sequences, and vendor-field leakage checks.","source_ids":["S1","S6","S7","S8"]},"bounded_next_evidence_step":{"status":"YES","reason":"A time-bounded, software-only two-simulator comparison can be completed without instrument motion and has pre-specifiable comparators, metrics, and falsifiers.","source_ids":["S1","S4"]},"no_unresolved_safety_or_authority_stop":{"status":"YES","reason":"The next step excludes every hardware transport and physical actuator. Any later hardware trial remains blocked pending instrument-owner and safety/quality authorization; simulator success cannot waive that boundary.","source_ids":["S3","S4"]},"credible_cost_scope_and_range":{"status":"YES","reason":"The ranges are broad resource-equivalent bands tied to explicit person-week, adapter-count, laboratory-count, and hardware-exclusion assumptions. Vendor quotations and time logs are absent, so deployment-band confidence remains low.","source_ids":["S1","S2","S4"]}},"next_evidence_step":"Run a pre-registered 10-week software-only differentiation trial. Comparator A is the existing afspm-style base-operation translator suite; comparator B is the candidate ProbeManipulationSession contract suite; comparator C is a generic SiLA/ROS-like action lifecycle without SPM-specific invariants. Before implementation, freeze the transition table, error catalog, side-effect matrix, and 24 seeded semantic mutants spanning premature completion, invalid-state motion, cancellation races, stale calibration, envelope escape, sensor loss, travel limit, post-FAULT motion, ambiguous and failed retraction, status-query side effects, and diagnostic leakage. Build two independent simulators with different queues, timing, and actuator models, with no hardware transport dependency. Run scripted cases, at least 10,000 generated sequences, and a held-out set written by an SPM expert who did not implement either simulator. Proceed only if the candidate detects every safety-critical mutant and at least 90% of all mutants, detects materially more than each comparator, has no held-out lifecycle/side-effect violation escape, accepts at least 95% of contract-preserving representation changes, and requires no vendor-specific public field. Falsify the incremental claim if a comparator performs equivalently, any safety-critical mutant escapes, valid implementations require controller-specific escape clauses, false rejection exceeds 5%, or any command can reach a hardware endpoint.","blocking_evidence":["No empirical comparison yet shows that the proposed SPM-specific contract catches defects missed by afspm's existing translator test suite.","No cross-laboratory prevalence estimate exists for controller-substitution incidents, tip/sample damage, or automation failures attributable specifically to under-specified interface semantics.","No named laboratory, vendor, or afspm maintainer has committed to adopt or govern the proposed contract.","Simulator conformance provides no evidence of emergency-stop, retraction, positioning, sensing, calibration, timing, or envelope performance on physical hardware.","Deployment and recurring costs lack vendor quotations, measured engineering time, instrument-downtime estimates, and quality-system requirements.","The completeness of normalized position uncertainty, calibration provenance, diagnostics, and modality-specific states remains unverified."],"research_disposition":"PARTNERED_RESEARCH_PROGRAM","world_novelty_boundary":"This evaluation measured neither world novelty, patentability, freedom to operate, market size, nor realized impact. The substantial-collision finding concerns only the eight reviewed sources: afspm already covers the closest domain architecture, while LADS, SiLA, and ROS establish adjacent state/action practices. A comprehensive literature, product, standards, source-code, and patent search could change the boundary.","arm":"COMPLETE_PROPOSAL_PORTFOLIO","candidate_version":0,"controller_recommendation":{"action":"STOP_EMPIRICAL_RESEARCH_NEEDED","repairable":false,"material_progress_observed":true,"progress_targets":["Complete the pre-registered two-simulator, three-comparator differentiation trial and publish per-mutant and held-out-sequence results.","Demonstrate that every safety-critical mutant is rejected and that the candidate materially outperforms afspm-style and generic-lifecycle comparators without vendor-specific public fields.","Obtain a written adoption inquiry from an afspm maintainer, SPM laboratory software steward, or controller vendor identifying which contract clauses solve an unmet integration problem.","Secure a written instrument-owner and laboratory safety/quality boundary before designing any hardware-connected follow-on.","Replace labor assumptions with measured time logs and obtain bottom-up estimates for two production adapters, qualification, downtime, training, and annual stewardship."],"reason":"Web evidence establishes a real problem, credible stakeholders, and implementability, but also reveals substantial collision with afspm and mature generic lifecycle standards. The only remaining defensible advantage—better detection of safety-relevant semantic non-substitutability—requires software experiments and expert-held-out testing, not more bounded web research."},"proposal_index":2}